I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 2 18:55:40 +14 2025 I: pbuilder-time-stamp: 1738472140 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [codonw_1.4.4-8.dsc] I: copying [./codonw_1.4.4.orig.tar.gz] I: copying [./codonw_1.4.4-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./codonw_1.4.4-8.dsc: unsupported subcommand dpkg-source: info: extracting codonw in codonw-1.4.4 dpkg-source: info: unpacking codonw_1.4.4.orig.tar.gz dpkg-source: info: unpacking codonw_1.4.4-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying enable_clean dpkg-source: info: applying remove_pause dpkg-source: info: applying define_linux dpkg-source: info: applying spelling dpkg-source: info: applying helpfile_location dpkg-source: info: applying fix_link_name_clashes dpkg-source: info: applying remove_nondeterminism dpkg-source: info: applying remove-gets.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31259/tmp/hooks/D01_modify_environment starting debug: Running on virt64b. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Feb 2 04:55 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/31259/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/31259/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=c404fd253de54e6cbb324d699c707275 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=31259 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.DM5L1nsu/pbuilderrc_y8B6 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.DM5L1nsu/b2 --logfile b2/build.log codonw_1.4.4-8.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/31259/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19573 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.7 MB of archives. After unpacking 74.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.23.1-1 [238 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.4-1 [84.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.23.1-1 [1560 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.24.1 [920 kB] Fetched 19.7 MB in 0s (63.5 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19573 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_armhf.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_armhf.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_armhf.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_armhf.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../21-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libunistring5:armhf. Preparing to unpack .../23-libunistring5_1.3-1_armhf.deb ... Unpacking libunistring5:armhf (1.3-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-6_armhf.deb ... Unpacking libicu72:armhf (72.1-6) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_armhf.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libicu72:armhf (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:armhf (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/31259/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/31259/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/codonw-1.4.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../codonw_1.4.4-8_source.changes dpkg-buildpackage: info: source package codonw dpkg-buildpackage: info: source version 1.4.4-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' rm -rf *.o *.coa *.blk *.out *raw codonw codonW.log make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' rm -rf debian/man dh_clean --exclude=Makefile.orig make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 codon_us.c cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 codons.c cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 open_fil.c cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 commline.c open_fil.c: In function 'open_file': open_fil.c:88:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fgets(infile_name, BUFSIZ, stdin); /* get filename */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c: In function 'main': codons.c:190:55: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 190 | fprintf(pm->my_err,"\n\n\t\tNumber of sequences: %i\n", | ~^ | | | int | %li 191 | num_sequence); | ~~~~~~~~~~~~ | | | long int open_fil.c:133:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 133 | fgets(answer, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ open_fil.c:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 166 | fgets(temp, 3, stdin); | ^~~~~~~~~~~~~~~~~~~~~ open_fil.c:186:21: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 186 | fgets(answer, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:196:32: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 196 | fprintf(pm->my_err, "\tWARNING\t At least one sequence in your" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 | " input file has\ninternal stop codons (found %i" 198 | " internal stops) \tWARNING\n",num_seq_int_stop); | ~~~~~~~~~~~~~~~~ | | | long int codons.c:197:68: note: format string is defined here 197 | " input file has\ninternal stop codons (found %i" | ~^ | | | int | %li codons.c:200:46: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 200 | fprintf(pm->my_err, "\tWARNING\t %i sequences had internal " | ~^ | | | int | %li 201 | "stop codons \tWARNING\n",num_seq_int_stop); | ~~~~~~~~~~~~~~~~ | | | long int open_fil.c:88:13: warning: 'fgets' writing 8192 bytes into a region of size 90 overflows the destination [-Wstringop-overflow=] 88 | fgets(infile_name, BUFSIZ, stdin); /* get filename */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ open_fil.c:71:12: note: destination object 'infile_name' of size 90 71 | char infile_name[MAX_FILENAME_LEN]=""; | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from open_fil.c:47: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ codons.c: In function 'toutput': codons.c:640:25: warning: unknown conversion type character '=' in format [-Wformat=] 640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:641:11: note: format string is defined here 641 | " =%5.3f\n" /* with G+C content and length of gene */ | ^ codons.c:647:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " | ~^ | | | int | %ld 648 | "in sequence %i\n" 649 | ,non_std_char - IUBC_TOT | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long int In file included from commline.c:28: commline.c: In function 'proc_comm_line': codons.c:647:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 650 | ,num_sequence); | ~~~~~~~~~~~~ | | | long int codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:103:9: note: in expansion of macro 'pause' 103 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:127:9: note: in expansion of macro 'pause' 127 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:142:9: note: in expansion of macro 'pause' 142 | pause; | ^~~~~ codons.c:648:25: note: format string is defined here 648 | "in sequence %i\n" | ~^ | | | int | %li codons.c:652:30: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 652 | fprintf(pm->my_err, "\t%3i>\t%6li %-40.40s\tPROTEIN\n" | ~~^ | | | int | %3li 653 | ,num_sequence | ~~~~~~~~~~~~ | | | long int codons.c:657:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 657 | fprintf(pm->my_err, "\t\t WARNING %d non " | ~^ | | | int | %ld ...... 660 | ,non_std_char | ~~~~~~~~~~~~ | | | long int codons.c:657:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 657 | fprintf(pm->my_err, "\t\t WARNING %d non " | ^~~~~~~~~~~~~~~~~~~~~~ ...... 661 | ,num_sequence); | ~~~~~~~~~~~~ | | | long int codons.c:659:25: note: format string is defined here 659 | "in sequence %i\n" | ~^ | | | int | %li codons.c: In function 'output': codons.c:800:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] 800 | fprintf(stderr, "ERROR-23 %s bulk undefined\n", pm->prog); | ~^ ~~~~~~~~ | | | | char * int | %d codons.c:805:32: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] 805 | fprintf(stderr, "ERROR-24 %s -prog undefined\n", pm->prog); | ~^ ~~~~~~~~ | | | | char * int | %d codon_us.c: In function 'codon_usage_out': codon_us.c:373:24: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 373 | fprintf(fblkout, "%i%c",nncod[x],sp); | ~^ ~~~~~~~~ | | | | int long int | %li codon_us.c: In function 'raau_usage_out': codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] 479 | fprintf(fblkout, "\n",sp); | ^~~~ In file included from codons.c:90: codons.c: In function 'main': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:204:35: note: in expansion of macro 'pause' 204 | if ( pm->codonW && pm->menu ) pause; | ^~~~~ codon_us.c: In function 'cbi_out': codon_us.c:831:32: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=] 831 | sprintf(pm->messages, " Serious error in CBI information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 836 | pcbi->fop_cod[x], x); | ~~~~~~~~~~~~~~~~ | | | int codon_us.c:832:38: note: format string is defined here 832 | " an illegal CBI value of %f for codon %i" | ~^ | | | double | %d codon_us.c: In function 'fop_out': codons.c: In function 'chelp': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1078:20: note: in expansion of macro 'pause' 1078 | pause; /* make sure they Ack. the error mesg */ | ^~~~~ codon_us.c:988:28: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 993 | pfop->fop_cod[x], x); | ~~~~~~~~~~~~~~~~ | | | int codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1097:35: note: in expansion of macro 'pause' 1097 | if ( line_counter )pause; | ^~~~~ codon_us.c:989:37: note: format string is defined here 989 | " an illegal fop value of %f for codon %l" | ~^ | | | double | %d codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1115:5: note: in expansion of macro 'pause' 1115 | pause; | ^~~~~ codon_us.c:988:28: warning: unknown conversion type character ' ' in format [-Wformat=] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1124:4: note: in expansion of macro 'pause' 1124 | pause; | ^~~~~ codon_us.c:990:11: note: format string is defined here 990 | " permissible values are \n 1 for non-optimal" | ^ codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1128:5: note: in expansion of macro 'pause' 1128 | pause; | ^~~~~ codon_us.c:994:25: warning: unknown conversion type character ',' in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^ codon_us.c:994:33: warning: unknown conversion type character ',' in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^ codon_us.c:994:44: warning: unknown conversion type character '\x0a' in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^~ codon_us.c:994:18: warning: too many arguments for format [-Wformat-extra-args] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'gc_out': codon_us.c:1181:10: warning: too many arguments for format [-Wformat-extra-args] 1181 | "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'dinuc_out': codon_us.c:1476:39: warning: precision used with '%c' gnu_printf format [-Wformat=] 1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp); | ^ In function 'fgets', inlined from 'open_file' at open_fil.c:88:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'hydro_out': codon_us.c:2115:27: warning: too many arguments for format [-Wformat-extra-args] 2115 | fprintf(pm->my_err, "No output was written to file \n", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'aromo_out': codon_us.c:2148:27: warning: too many arguments for format [-Wformat-extra-args] 2148 | fprintf(pm->my_err, "No output was written to file \n", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from codon_us.c:77: codon_us.c: In function 'codon_error': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:347:6: note: in expansion of macro 'pause' 347 | pause; | ^~~~~ codon_us.c: In function 'cai_out': codon_us.c:652:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 652 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'cbi_out': codon_us.c:759:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 759 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'fop_out': codon_us.c:899:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 899 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:957:14: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 957 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'gen_cusort_fop': codon_us.c:1699:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1699 | fgets(pm->junk, BUFSIZ,fnam);/* by scanning for lines of CU in */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1700:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1700 | fscanf(fnam, "%s", pm->junk); /* now we know the name of seq i */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1703:8: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1703 | fscanf(fnam, "%f", &v2); /* assign it initially to v2 */ | ^~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1711:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1711 | fscanf(fnam, "%f\n", &v2); /* now read the last codon in */ | ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 menu.c In file included from menu.c:31: menu.c: In function 'main_menu': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:69:9: note: in expansion of macro 'pause' 69 | pause; | ^~~~~ menu.c: In function 'menu_initial': menu.c:106:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:122:29: note: in expansion of macro 'pause' 122 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:132:17: note: in expansion of macro 'pause' 132 | pause; | ^~~~~ menu.c: In function 'menu_2': menu.c:233:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 233 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:250:17: note: in expansion of macro 'pause' 250 | pause; | ^~~~~ menu.c: In function 'menu_3': menu.c:305:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:322:17: note: in expansion of macro 'pause' 322 | pause; | ^~~~~ menu.c:345:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 345 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:382:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 382 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:401:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 401 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:425:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:450:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 450 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_4': menu.c:580:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 580 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:620:17: note: in expansion of macro 'pause' 620 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:640:17: note: in expansion of macro 'pause' 640 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:660:17: note: in expansion of macro 'pause' 660 | pause; | ^~~~~ menu.c: In function 'menu_5': menu.c:764:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 764 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:814:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 814 | fgets( pm->junk , BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_6': menu.c:844:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 844 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:861:17: note: in expansion of macro 'pause' 861 | pause; | ^~~~~ menu.c: In function 'menu_7': menu.c:893:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 893 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:912:17: note: in expansion of macro 'pause' 912 | pause; | ^~~~~ menu.c: In function 'menu_8': menu.c:975:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 975 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1007:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1007 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1024:11: note: in expansion of macro 'pause' 1024 | pause; | ^~~~~ menu.c: In function 'menu_coa': menu.c:1067:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1067 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1085:9: note: in expansion of macro 'pause' 1085 | pause; | ^~~~~ menu.c:1097:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1097 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1117:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1117 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1130:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1130 | fgets ( pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'select_coa': menu.c:1224:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1224 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=] 620 | printf("Could not open input file - %s\n", p ); | ^~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 tester.c tester.c: In function 'tester': tester.c:88:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fgets( pm->junk , BUFSIZ, stdin) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:125:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fgets( pm->junk , BUFSIZ, stdin) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:170:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 170 | fgets( pm->junk , BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tester.c:48: tester.c: In function 'asummary': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:235:5: note: in expansion of macro 'pause' 235 | pause; | ^~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c coresp.c: In function 'textbin': coresp.c:98:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 98 | fscanf(pm->fcoa_in,"%s",pm->junk); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:104:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 104 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:108:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 108 | fscanf(pm->fcoa_in,"%i\n",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:115:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:119:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | fscanf(pm->fcoa_in,"%i\n",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:127:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:131:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | fscanf(pm->fcoa_in,"%i\n",&v2); /* read last codon */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function 'rowout': coresp.c:277:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function 'inertialig': coresp.c:1271:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1271 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:1315:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1315 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function 'suprow': coresp.c:1619:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1619 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -Wl,-z,relro -Wl,-z,now codon_us.o codons.o open_fil.o commline.o menu.o tester.o coresp.o -o codonw -lm make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' mkdir -p debian/codonw/usr/bin cp codonw debian/codonw/usr/bin mkdir -p debian/codonw/usr/share/codonw cp codonW.hlp debian/codonw/usr/share/codonw chmod -x debian/codonw/usr/share/codonw/codonW.hlp make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_install debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' mkdir -p debian/codonw/usr/share/doc/codonw cp *.txt debian/codonw/usr/share/doc/codonw dh_installdocs -- make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' mkdir -p /build/reproducible-path/codonw-1.4.4/debian/man /build/reproducible-path/codonw-1.4.4/debian/make_man.pl /build/reproducible-path/codonw-1.4.4/debian/template.man \ /build/reproducible-path/codonw-1.4.4/debian/man calculate Amino Acid Usage (AAU) clean up sequence in FASTA format GC of synonymous codons 3rd positions calculate Relative Synonymous Codon Usage (RSCU) conceptual translation of DNA to amino acid calculate Codon Adaptation Index (CAI) calculate Frequency of OPtimal codons index (FOP) dinucleotide usage of the three codon positions detailed report of base composition calculate Relative Amino Acid Usage (RAAU) tabulation of codon usage silent base G+C+A+T calculating program G+C content of gene (all 3 codon positions) calculate Codon Bias Index (CBI) calculate Effective Number of Codons (ENc) tabulation of datasets codon usage calculate codon usage output sequence in reader format dh_installman -- make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' dh_fixperms chmod -x debian/codonw/usr/share/doc/codonw/examples/input.dat make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'codonw' in '../codonw_1.4.4-8_armhf.deb'. dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../codonw_1.4.4-8_armhf.buildinfo dpkg-genchanges --build=binary -O../codonw_1.4.4-8_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/31259/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/31259/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/31259 and its subdirectories I: Current time: Sun Feb 2 18:56:29 +14 2025 I: pbuilder-time-stamp: 1738472189